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Package 39/319HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.8.0
Ernest Turro
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/bgx
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: bgx
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes bgx_1.8.0.tar.gz
StartedAt: 2009-10-20 17:02:32 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:06:26 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 233.2 seconds
RetCode: 0
Status: OK
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/bgx.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bgx' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

bgx.Rcheck/00install.out:

* Installing *source* package ‘bgx’ ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin8.11.1
checking host system type... i386-apple-darwin8.11.1
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... unknown
checking for x86 cpuid 1 output... unknown
checking for gcc architecture flag... unknown
checking for gcc -arch i386 -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... no
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 

** help
*** installing help indices
 >>> Building/Updating help pages for package 'bgx'
     Formats: text html latex example 
Note: removing empty section \examples in file 'analysis.bgx.Rd'
  analysis.bgx                      text    html    latex
  bgx                               text    html    latex   example
Note: removing empty section \examples in file 'mcmc.bgx.Rd'
  mcmc.bgx                          text    html    latex
Note: removing empty section \examples in file 'readOutput.bgx.Rd'
  readOutput.bgx                    text    html    latex
Note: removing empty section \value in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \details in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \examples in file 'saveAffinityPlot.bgx.Rd'
  saveAffinityPlot.bgx              text    html    latex
Note: removing empty section \details in file 'setupVars.bgx.Rd'
Note: removing empty section \examples in file 'setupVars.bgx.Rd'
  setupVars.bgx                     text    html    latex
** building package indices ...
* DONE (bgx)